TypeError: cannot pickle '_thread.lock' object #614
Description
Discussed in https://github.com/corteva/rioxarray/discussions/613
Originally posted by pradeeps31 December 8, 2022
Hi Guys,
I am trying to convert a netCDF file to GeoTIFF file using xarrray and rioxarray. But when I give the rio.to_raster command, it throws the TypeError: cannot pickle '_thread.lock' object. The NetCDF file (.nc4) is a precipitation dataset downloaded from NASA Earthdata. The code I have used is below:
>>> import xarray as xr
>>> import rioxarray as rio
>>> ncfile = xr.open_dataset('3B-DAY.MS.MRG.3IMERG.20210901-S000000-E235959.V06.nc4')
>>> pr = ncfile['precipitationCal']
>>> pr = pr.transpose('time', 'lat', 'lon')
>>> pr = pr.rio.set_spatial_dims('lon', 'lat')
>>> pr.rio.crs
>>> pr.rio.crs
>>> pr.rio.set_crs("epsg:4326")
<xarray.DataArray 'precipitationCal' (time: 1, lat: 1800, lon: 3600)>
[6480000 values with dtype=float32]
Coordinates:
* lon (lon) float32 -179.9 -179.8 -179.8 -179.6 ... 179.8 179.9 179.9
* lat (lat) float32 -89.95 -89.85 -89.75 -89.65 ... 89.75 89.85 89.95
* time (time) object 2021-09-01 00:00:00
Attributes:
units: mm
long_name: Daily accumulated precipitation (combined microwave-IR) estimate
>>> pr.rio.to_raster(r"trial1.tif")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\site-packages\rioxarray\raster_array.py", line 1145, in to_raster
return RasterioWriter(raster_path=raster_path).to_raster(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\site-packages\rioxarray\raster_writer.py", line 232, in to_raster
xarray_dataarray = xarray_dataarray.copy()
^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\site-packages\xarray\core\dataarray.py", line 1181, in copy
return self._copy(deep=deep, data=data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\site-packages\xarray\core\dataarray.py", line 1189, in _copy
variable = self.variable._copy(deep=deep, data=data, memo=memo)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\site-packages\xarray\core\variable.py", line 1048, in _copy
ndata = copy.deepcopy(ndata, memo)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in _deepcopy_tuple
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in <listcomp>
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in _deepcopy_tuple
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in <listcomp>
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in _deepcopy_tuple
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in <listcomp>
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in _deepcopy_tuple
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in <listcomp>
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 172, in deepcopy
y = _reconstruct(x, memo, *rv)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 271, in _reconstruct
state = deepcopy(state, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 231, in _deepcopy_dict
y[deepcopy(key, memo)] = deepcopy(value, memo)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 146, in deepcopy
y = copier(x, memo)
^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in _deepcopy_tuple
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 211, in <listcomp>
y = [deepcopy(a, memo) for a in x]
^^^^^^^^^^^^^^^^^
File "C:\Users\Pradeep\anaconda3\envs\imerg_env\Lib\copy.py", line 161, in deepcopy
rv = reductor(4)
^^^^^^^^^^^
TypeError: cannot pickle '_thread.lock' object
>>>
Could anyone help me to resolve this issue. I'm using python 3.11 version.
Thanks
Pradeep